DNA and RNA hybridization probes, for use in the clinical diagnosis of infectious disease agents and for genetic screening, are under intensive commercial development. Hybridization probes, either chemically synthesized or derived from natural or recombinant DNA sources, have been shown to be highly specific in the detection and identification of a variety of viruses and bacteria. Synthetic oligonucleotides have also been shown to be useful in detecting genetic abnormalities in a Southern blot format. However, nearly all current methods for the use of hybridization probes require extensive sample preparation, followed by gel-electrophoresis or immobilization on filters, hybridization for up to 24 hours and protracted secondary procedures for detection. These procedures are tedious, time consuming and highly specialized techniques which are not easily automated. In addition, the most senitive detection techniques rely on radioactivity which presents both handling and disposal problems in the clinical lab. There is a need for an efficient, rapid, easily automatable hybridization analysis system which can be applied to relatively crude samples and is compatible with current non-isotopic detection methodologies.